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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
India
Mexico
Russia
Peru
Indonesia
United Kingdom
Italy
Colombia
Iran
France
Argentina
Germany
South Africa
Spain
Poland
Turkey
Ukraine
Philippines
Romania
Chile
Ecuador
Czechia
Hungary
Canada
Pakistan
Bangladesh
Malaysia
Belgium
Tunisia
Iraq
Bulgaria
Vietnam
Bolivia
Netherlands
Burma
Portugal
Japan
Egypt
Thailand
Kazakhstan
Paraguay
Greece
Sweden
Morocco
Guatemala
Sri Lanka
Slovakia
Nepal
Switzerland
Austria
Bosnia and Herzegovina
Jordan
Honduras
Georgia
Croatia
Saudi Arabia
Serbia
Lebanon
Israel
Cuba
Panama
Afghanistan
Moldova
North Macedonia
Azerbaijan
Costa Rica
Uruguay
Ethiopia
Algeria
Armenia
Ireland
Lithuania
Kenya
Slovenia
Libya
China
Zimbabwe
Venezuela
West Bank and Gaza
Belarus
Oman
Dominican Republic
Zambia
Namibia
El Salvador
Uganda
Kosovo
Sudan
Latvia
Albania
Nigeria
Denmark
Kyrgyzstan
South Korea
Cambodia
Kuwait
Botswana
Syria
Malawi
United Arab Emirates
Jamaica
Montenegro
Mozambique
Senegal
Angola
Trinidad and Tobago
Cameroon
Mongolia
Australia
Estonia
Bahrain
Rwanda
Uzbekistan
Eswatini
Somalia
Ghana
Finland
Congo (Kinshasa)
Suriname
Madagascar
Norway
Taiwan*
Guyana
Luxembourg
Mauritania
Tanzania
Cote d'Ivoire
Fiji
Lesotho
Haiti
Qatar
Bahamas
Cyprus
Mali
Malta
Belize
Guinea
Cabo Verde
Papua New Guinea
Togo
Maldives
Saint Lucia
Hong Kong
Congo (Brazzaville)
Nicaragua
Gabon
Burkina Faso
Djibouti
Singapore
Benin
Equatorial Guinea
Andorra
South Sudan
Tajikistan
Timor-Leste
Seychelles
Mauritius
Central African Republic

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
India
Mexico
Russia
Peru
Indonesia
United Kingdom
Italy
Colombia
Iran
France
Argentina
Germany
South Africa
Spain
Poland
Turkey
Ukraine
Philippines
Romania
Chile
Ecuador
Czechia
Hungary
Canada
Pakistan
Bangladesh
Malaysia
Belgium
Tunisia
Iraq
Bulgaria
Vietnam
Bolivia
Netherlands
Burma
Portugal
Japan
Egypt
Thailand
Kazakhstan
Paraguay
Greece
Sweden
Morocco
Guatemala
Sri Lanka
Slovakia
Nepal
Switzerland
Austria
Bosnia and Herzegovina
Jordan
Honduras
Georgia
Croatia
Saudi Arabia
Serbia
Lebanon
Israel
Cuba
Panama
Afghanistan
Moldova
North Macedonia
Azerbaijan
Costa Rica
Uruguay
Ethiopia
Algeria
Armenia
Ireland
Lithuania
Kenya
Slovenia
Libya
China
Zimbabwe
Venezuela
West Bank and Gaza
Belarus
Oman
Dominican Republic
Zambia
Namibia
El Salvador
Uganda
Kosovo
Sudan
Latvia
Albania
Nigeria
Denmark
Kyrgyzstan
South Korea
Cambodia
Kuwait
Botswana
Syria
Malawi
United Arab Emirates
Jamaica
Montenegro
Mozambique
Senegal
Angola
Trinidad and Tobago
Cameroon
Mongolia
Australia
Estonia
Bahrain
Rwanda
Uzbekistan
Eswatini
Somalia
Ghana
Finland
Congo (Kinshasa)
Suriname
Madagascar
Norway
Taiwan*
Guyana
Luxembourg
Mauritania
Tanzania
Cote d'Ivoire
Fiji
Lesotho
Haiti
Qatar
Bahamas
Cyprus
Mali
Malta
Belize
Guinea
Cabo Verde
Papua New Guinea
Togo
Maldives
Saint Lucia
Hong Kong
Congo (Brazzaville)
Nicaragua
Gabon
Burkina Faso
Djibouti
Singapore
Benin
Equatorial Guinea
Andorra
South Sudan
Tajikistan
Timor-Leste
Seychelles
Mauritius
Central African Republic